Search

Scale and hierarchy have received less attention in aquatic compared to terrestrial systems. Walleye (Sander vitreus) spawning habitat offers an opportunity to investigate scale's importance. We estimated lake-, transect-, and quadrat-scale influences on nearshore walleye egg deposition in 28 Minnesota lakes from 2016-2018. Random forest models (RFM) estimated importance of predictive variables to walleye egg deposition. Predictive accuracies of a multi-scale classification tree (CT) and a quadrat-scale CT were compared. RFM results suggested that five of our variables were unimportant when predicting egg deposition. The multi-scale CT was more accurate than the quadrat-scale CT when predicting egg deposition. Both model results suggest that in-lake egg deposition by walleye is regulated by hierarchical abiotic processes and that silt-clay abundance at the transectscale (reef-scale) is more important than abundance at the quadrat-scale (within-reef). Our results show machine learning can be used for scale-optimization and potentially to determine cross-scale interactions. Further incorporation of scale and hierarchy into studies of aquatic systems will increase our understanding of species-habitat relationships, especially in lentic systems where multi-scale approaches are rarely used. Moins d'attention est accordee a l'echelle et a la hierarchie dans l'etude des systemes aquatiques que dans celle des systemes terrestres. L'habitat de frai du dore jaune (Sander vitreus) offre l'occasion d'etudier l'importance de l'echelle. Nous estimons les influences a l'echelle du lac, du transect et du quadrat sur la ponte pres du rivage de dores dans 28 lacs du Minnesota de 2016 a 2018. Des modeles de foret aleatoire (MFA) permettent d'estimer l'importance de variables predictives pour la ponte des dores. L'exactitude des predictions d'un arbre de classification (AC) multiechelle et d'un AC a l'echelle du quadrat a ete comparee. Les resultats des MFA donnent a penser que cinq des variables examinees ne sont pas importantes pour la prediction de la ponte. L'AC multiechelle est plus exact que l'AC a l'echelle du quadrat pour la prediction de la ponte. Les resultats des deux modeles indiqueraient que la ponte en lac par les dores est modulee par des processus abiotiques hierarchiques et que l'abondance de limon-argile a l'echelle du transect (echelle du recif) est plus importante que l'abondance a l'echelle du quadrat (intra-recif). Nos resultats montrent que l'apprentissage automatique peut etre utilise pour l'optimisation de l'echelle et, eventuellement, pour cerner les interactions inter-echelles. L'integration plus poussee de l'echelle et de la hierarchie dans les etudes de systemes aquatiques rehaussera la comprehension des relations especes-habitats, particulierement dans les systemes lentiques pour lesquels des approches multiechelles sont rarement utilisees. [Traduit par la Redaction], Introduction The spatial unit at which an ecological phenomenon is observed or measured is referred to as 'scale' in ecological literature. The importance of scale when observing an ecological phenomenon [...]

Background and Aim: This study aimed to compare the determinants and impact of hepatocellular carcinoma (HCC) surveillance rates for people with metabolic dysfunction‐associated steatotic liver disease (MASLD) versus other chronic liver diseases. Methods: A dataset of HCC patients from a UK hospital (2007–2022) was analyzed. The Mann–Whitney U‐test compared continuous variables. The χ2 and two‐tailed Fisher exact tests compared categorical data. Regression modeling analyzed the impact of MASLD on the size and number of HCC nodules and curative treatment. The Cox proportional hazards model assessed the influence of MASLD on overall survival. Results: A total of 176 of 687 (25.6%) HCC patients had MASLD. Fewer people with MASLD HCC were enrolled in HCC surveillance compared to non‐MASLD HCC (38 [21.6%] vs 215 [42.1%], P < 0.001). Patients with MASLD HCC were less likely to have been under secondary care (n = 57 [32.4%] vs 259 [50.7%], P < 0.001) and less likely to have cirrhosis (n = 113 [64.2%] vs 417 [81.6%], P < 0.001). MASLD was associated with a 12.3‐mm (95% confidence interval [CI] 10.8–14.0 mm) greater tumor diameter compared to people without MASLD (P = 0.002). Patients with MASLD HCC had 0.62 reduced odds (95% CI 0.43–0.91) of receiving curative treatment compared to non‐MASLD HCC (P = 0.014). Overall survival was similar for patients with MASLD HCC versus non‐MASLD HCC (hazard ratio 1.03, 95% CI 0.85–1.25, P = 0.748). Conclusion: Patients with MASLD are less likely to have been enrolled in HCC surveillance due to undiagnosed cirrhosis or presenting with non‐cirrhotic HCC. Patients with MASLD HCC present with larger tumors and are less likely to receive curative treatment. [ABSTRACT FROM AUTHOR]

Oxygen plays a central role in biomolecular structures and functions, with 17O NMR emerging as a powerful tool for elucidating biomolecular properties. However, the low natural abundance of the NMR‐active isotope, 17O (0.0373 %), presents a significant hurdle to its widespread application. Here, we introduce a rapid and cost‐effective approach for amino acid‐specific 17O‐labeling of recombinant proteins. Using a common bacterial expression system and with a 30‐minute rapid synthesis protocol of 17O‐labeled amino acids via mechanochemical saponification, we have generated Leu‐ and Phe‐specific 17O‐labeled recombinant proteins derived from diverse organisms, including CrgA and FtsQ from Mycobacterium tuberculosis and E protein from SARS‐CoV‐2 virus, demonstrating the applicability of our technique for amino acids known to be isotopically labeled without scrambling. We have acquired magic‐angle‐spinning 17O NMR of these proteins to confirm the successful 17O labeling and illustrate the sensitivity of 17O NMR to the protein's local structural environments. Our work significantly broadens the accessibility of 17O‐NMR, empowering researchers to delve deeper into protein biophysics and biochemistry. This approach opens new avenues for understanding cellular processes at the molecular level by providing an effective tool for investigating oxygen‐related interactions and chemistry within biomolecules. [ABSTRACT FROM AUTHOR]

CrgA is a key transmembrane (TM) protein in the cell division process of Mycobacterium tuberculosis ( Mtb ), the pathogen responsible for tuberculosis. While many of the Mtb divisome proteins have been identified, their structures and interactions remain largely unknown. Previous studies of CrgA using oriented-sample solid-state NMR have defined the tilt and rotation of the TM helices, but the cytoplasmic and periplasmic domains and even the oligomeric state were uncharacterized. Here, combining oriented-sample and magic-angle spinning solid-state NMR spectra, we solved the full-length structure of CrgA. The structure features a dimer with a TM domain sandwiched between a cytoplasmic β-sheet and a periplasmic β-sheet. The β-sheets stabilize dimerization, which in turn increases CrgA's ability to participate in multiple protein interactions. Within the membrane, CrgA binds FtsQ, CwsA, PbpA, FtsI, and MmPL3 via its TM helices; in the cytoplasm, Lys23 and Lys25 project outward from the β-sheet to interact with acidic residues of FtsQ and FtsZ. The structural determination of CrgA thus provides significant insights into its roles in recruiting other divisome proteins and stabilizing their complexes for Mtb cell wall synthesis and polar growth.

The SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein has been found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identified only a symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions., Competing Interests: Competing interests The authors declare no competing interests.